By Bernard M. E. Moret (auth.), Aaron Darling, Jens Stoye (eds.)
This publication constitutes the refereed court cases of the thirteenth foreign Workshop on Algorithms in Bioinformatics, WABI 2013, held in Sophia Antipolis, France, in September 2013. WABI 2013 is one in every of seven workshops which, besides the eu Symposium on Algorithms (ESA), represent the ALGO annual assembly and highlights learn in algorithmic paintings for bioinformatics, computational biology and structures biology. The objective is to provide contemporary learn effects, together with major work-in-progress, and to spot and discover instructions of destiny learn. The 27 complete papers awarded have been rigorously reviewed and chosen from sixty one submissions. The papers disguise all facets of algorithms in bioinformatics, computational biology and structures biology.
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Extra info for Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings
Note that the optimal ROTRAN that maximizes the alignment score is located in the largest cluster, which includes 13% of the initially sampled ROTRANs. Therefore, our search algorithm is highly eﬃcient because the alignment score calculation (by the computationally expensive dynamic programming algorithm) for noise ROTRANs is mainly 22 X. Cui et al. (a) ROTRANs initially sampled (b) ROTRANs of the four largest clusters Fig. 1. ROTRANs before and after clustering when aligning SCOP domains d3k2aa and d2cufa1: each ROTRAN is represented by a coordinate that is calculated by applying the rotation matrix of the ROTRAN on coordinate (1, 0, 0) eliminated.
Speciﬁcally, two L9R3align F-scores equal to 100% and 19 L9R3align F-scores are higher than 50%. For the two cases that L9R3align F-scores are equal to 100%, the aligned protein structures contain a high percentage of helices, and TMalign shifts the HOMSTRAD alignment by a few residues, which has also been previously observed . Such shifting is diﬃcult to avoid by evaluating only structure similarities. However, the shifting is avoided by our scoring function, involving both structure and sequence similarities, in this experiment.
3, we compared our scoring function to TM-score  to demonstrate that our method tends to ﬁnd alignments more consistent with the eye-examined alignments in HOMSTRAD . 1 Search Algorithm Evaluation on TM-Score To demonstrate reliability, we repeated the alignment experiment for the 200 non-homologous protein structures, which have sizes of between 46 and 1058, have a sequence identity cutoﬀ of 30%, and are used by TM-align . We compared our results with that of current methods, TM-align and fr-TM-align .
Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings by Bernard M. E. Moret (auth.), Aaron Darling, Jens Stoye (eds.)